A couple of things can kill the bees in the vac.
1. Too much suction, this is a huge killer of the bees. Use only enough to get them into the hose. If you are sucking them up and it sounds like marbles banging down the hose they will be dead (mostly broken in half) by the time they hit the hive body.
2. Over heating, this is also a huge killer of the bees. If you used only enough suction to get them into the hive body they need air to stay alive. If I turn my vac off I pull the top sliding panel out immediately. Give them some water, use a spray bottle, dribble it over the screen from a straw, shake a little in from a water bottle. Not only do they drink it but spread it around and fan it to cool the hive. Over heated bees will look greasy.
3. Sucking up nectar and honey it a killer also. Bees can become coated in sticky nectar and honey with no way to clean themselves and more or less suffocate. Care should be taken when using the vac on the face of honey comb, especially when filled with nectar, the vac will suck it out of the comb coating the inside of your hose and all of the bees that enter the hose. I have stopped and washed out the end of my hose before. You will find bees all coated with the sticky stuff in a wad on the bottom of the vac.
I guess this is telling on myself, and yes I have killed what looked like the whole cut out before, very sad after you spend all day trying to save a hive of bees.